The UWCCC Proteomics Shared Service is incorporated in the University of Wisconsin Biotechnology Center (UWBC) Mass Spectrometry Facility. The goal is to provide UWCCC researchers access to state of the art mass spectrometry and gel electrophoresis instrumentation for proteomic and metabolomics research. In addition they will be able to access tools and expertise to help with experimental design and data interpretation. This Facility will facilitate and enhance the scientific productivity of UWCCC members as they begin to use these new and advancing proteomic and metabolomic technologies. Current technologies include a Sciex 4800 TOF/TOF Micromass ESI Q-TOF2 hybrid mass spectrometer, a Sciex 3200 QTrap, a Bruker BIFLEX III MALDI-TOF, an Agilent LC/MSD TOF, and an Agilent 1100 series LC/MSD Trap SL ion trap for the analysis of biomolecules, including proteins, DNA, RNA, peptides, oligonucleotides, oligosaccharides and other small organic and inorganic molecules. In addition to measuring the molecular weight of compounds, the instruments are designed to perform MS/MS so that the structure of a selected ion can be deduced from the fragments. This is particularly useful for peptide sequencing and post-translational modification mapping. The four ESI-MS are equipped with HPLC systems for LC/MS/MS experiments. LC/MS/MS is extremely useful for quantitation of known compounds and for the rapid screening of a mixture to identify the components of interest. Capability exists to perform proteolytic digestions of proteins, which can be further analyzed by HPLC, MS, LC/MS and MS/MS for peptide mapping and peptide sequencing. The Mass Spectrometry/Proteomics/Metabolomics Facility is utilized in many ways to support cancer related research. These range from routine measurements of synthetic compounds to specialized projects targeting biomarkers. The facility can adapt to address new projects as they are conceived. This usage has steadily increased over the past several years, and will increase in the future as human and other genomic databases are expanded.